Some topoisomerase inhibitors trap covalent topoisomerase-DNA complexes as topoisomerase-drug-DNA ternary complexes. Ternary complex formation results in inhibition of DNA replication and generation of permanent double-strand breaks. Recent demonstrations of the stimulation of covalent topoisomerase-DNA complex formation by DNA lesions suggest that DNA damage may act as an endogenous topoisomerase poison. We have investigated the effects of abasic (AP) sites on topoisomerase IV (Topo IV). AP sites can stimulate the formation of covalent Topo IV-DNA complexes when they are located either within the 4 base overhang generated by DNA scission or immediately 5′ to the point of scission (the -1 position). Thus, the AP site acts as a position-specific, endogenous topoisomerase poison. Both EDTA and salt can reverse covalent Topo IV-DNA complexes induced by AP sites located within the 4 base overhang. Interestingly, an AP site at the-1 position inhibits EDTA-mediated reversal of formation of the covalent Topo IV-DNA complex. Furthermore, we find that, unlike quinolone-induced covalent Topo IV-DNA complexes, AP site-induced covalent Topo IV-DNA complexes do not inhibit the helicase activities of the DnaB and T7 Gene 4 proteins. These results suggest that the AP site-induced poisoning of Topo IV does not arrest replication fork progression.